Contacts of the helix formed by residues 133 - 148 (chain B) in PDB entry 1U1C
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B VAL 4.0 0.6 + - - -
132B ALA* 1.3 70.3 - - - +
134B PHE* 1.3 60.7 + - - +
135B GLU* 3.1 30.2 + - - +
136B CYS* 3.1 17.5 + - - +
137B THR* 3.0 30.5 + - - -
207B ALA* 6.2 0.2 - - - +
211B LEU 5.2 1.3 - - - +
212B ARG* 3.6 28.3 - - - +
213B ALA* 2.9 32.1 + - - +
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Residues in contact with PHE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ALA 3.6 3.7 + - - -
133B ASP* 1.3 75.8 + - - +
135B GLU* 1.3 67.1 + - + +
137B THR* 3.4 4.7 + - - -
138B THR* 2.9 51.2 + - + -
111F THR* 4.1 10.3 - - + +
134F PHE* 4.2 11.7 - + - -
137F THR* 3.9 28.9 - - + -
138F THR* 3.7 36.8 - - + -
141F VAL* 4.0 27.4 - - + -
153F VAL* 4.1 27.4 - - + -
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASP* 3.1 10.2 + - - +
134B PHE* 1.3 85.7 - - + +
136B CYS* 1.3 58.0 + - - +
138B THR* 3.5 6.9 + - - -
139B ALA* 3.0 28.8 + - - +
212B ARG* 2.8 43.1 + - - +
252B LEU* 3.8 7.3 - - + +
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Residues in contact with CYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B THR* 3.8 20.4 - - - -
90B LEU* 4.1 5.2 - - + +
133B ASP* 3.1 19.2 + - - +
134B PHE 3.3 0.2 - - - -
135B GLU* 1.3 75.4 - - - +
137B THR* 1.3 58.6 - - - +
139B ALA* 3.4 2.4 + - - +
140B LEU* 3.0 35.3 + - - +
212B ARG* 3.8 21.8 - - - -
213B ALA 3.6 28.0 - - - +
214B GLY* 3.7 11.0 - - - -
252B LEU* 4.0 16.4 - - - -
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Residues in contact with THR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B VAL* 3.9 20.4 - - + +
110B THR 4.0 3.0 + - - +
111B THR* 4.5 16.3 - - + -
132B ALA* 3.4 22.2 + - - +
133B ASP 3.0 18.3 + - - -
134B PHE* 3.7 6.7 - - - -
136B CYS* 1.3 72.7 - - - +
138B THR* 1.3 59.7 + - - +
140B LEU* 3.3 7.8 + - - +
141B VAL* 2.9 36.9 + - + +
153B VAL* 4.9 0.7 - - + -
214B GLY* 5.0 0.9 - - - -
215B MET 5.7 0.2 + - - -
134F PHE* 3.8 26.0 - - + -
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Residues in contact with THR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B PHE* 2.9 46.2 + - + -
135B GLU* 3.6 7.6 - - - -
136B CYS 3.3 0.2 - - - -
137B THR* 1.3 76.1 - - - +
139B ALA* 1.3 57.3 + - - +
141B VAL* 3.3 2.3 + - - +
142B GLU* 2.8 51.1 + - + +
134F PHE* 3.8 18.5 - - + -
138F THR* 5.0 2.9 + - + +
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLU 3.0 18.5 + - - +
136B CYS 3.7 4.5 - - - +
138B THR* 1.3 75.6 - - - +
140B LEU* 1.3 56.8 + - - +
142B GLU* 3.9 3.8 - - - +
143B ALA* 2.9 31.0 + - - +
248B ALA* 3.5 26.1 - - + +
251B ARG* 4.1 19.7 - - + +
252B LEU* 3.7 17.5 - - + -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU* 4.1 7.0 - - + -
91B ARG 5.5 0.7 - - - +
109B VAL* 4.0 18.3 - - + +
136B CYS 3.0 20.9 + - - +
137B THR* 3.7 5.4 - - - +
138B THR 3.3 0.2 - - - -
139B ALA* 1.3 73.7 - - - +
141B VAL* 1.3 61.1 + - - +
143B ALA* 4.4 0.4 - - - -
144B ALA* 3.1 26.5 + - - +
214B GLY* 3.8 9.4 - - - -
215B MET 3.5 39.5 - - - +
216B VAL* 3.7 26.0 - - + -
244B ILE* 3.7 16.3 - - + +
245B VAL* 4.2 11.2 - - + -
248B ALA* 3.7 21.8 - - + -
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B VAL* 4.1 13.7 - - + -
137B THR* 2.9 24.6 + - + +
138B THR 3.7 3.4 - - - +
140B LEU* 1.3 74.6 - - - +
142B GLU* 1.3 65.9 + - + +
144B ALA* 3.4 15.6 + - - +
145B LYS* 3.4 12.0 + - - +
151B THR* 5.6 2.2 - - + -
153B VAL* 3.9 28.9 - - + -
134F PHE* 4.1 28.5 - - + -
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B THR* 2.8 39.3 + - + +
139B ALA* 3.9 5.0 - - - +
141B VAL* 1.3 79.8 - - + +
143B ALA* 1.3 56.6 + - - +
145B LYS* 3.3 9.1 + - - +
146B SER* 3.1 23.9 + - - -
251B ARG* 3.7 37.7 + - - +
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ALA 2.9 20.4 + - - +
140B LEU 4.0 3.8 - - - +
141B VAL 3.3 0.2 - - - -
142B GLU* 1.3 74.6 - - - +
144B ALA* 1.3 63.7 + - - +
146B SER* 3.2 17.8 + - - -
147B ILE* 3.3 19.6 + - - +
244B ILE* 3.4 28.9 - - + +
247B GLU* 3.8 10.9 - - + +
248B ALA* 3.5 13.9 - - + +
251B ARG* 4.1 2.9 - - - +
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B VAL* 4.6 0.4 - - + -
109B VAL* 5.3 0.9 - - + -
140B LEU 3.1 14.8 + - - +
141B VAL 3.5 11.4 - - - +
142B GLU 3.3 0.4 - - - -
143B ALA* 1.3 78.8 - - - +
145B LYS* 1.3 56.2 + - - +
147B ILE* 3.9 1.6 + - - +
148B GLY 3.1 6.1 + - - -
149B ALA 3.0 29.0 + - - +
151B THR* 3.3 35.7 - - + +
244B ILE* 3.6 21.5 - - + +
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Residues in contact with LYS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B VAL 3.4 7.8 + - - +
142B GLU* 3.3 11.5 + - - +
143B ALA 3.2 0.4 - - - -
144B ALA* 1.3 77.6 - - - +
146B SER* 1.3 65.0 + - - +
148B GLY* 3.3 13.3 + - - +
149B ALA 5.6 0.7 - - - -
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B GLU 3.1 7.1 + - - -
143B ALA* 3.2 13.0 + - - -
145B LYS* 1.3 77.6 - - - +
147B ILE* 1.3 58.2 + - - +
247B GLU* 3.8 20.3 + - - +
251B ARG* 3.5 29.3 + - - -
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Residues in contact with ILE 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ALA 3.3 8.9 + - - +
144B ALA 3.9 3.8 - - - +
146B SER* 1.3 80.0 - - - +
148B GLY* 1.3 62.7 + - - +
149B ALA* 3.8 7.6 - - + -
240B HIS* 3.5 58.3 - - + +
243B LYS* 4.3 34.8 - - + +
244B ILE* 3.6 16.8 - - + -
247B GLU* 4.7 11.2 - - + +
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Residues in contact with GLY 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B ALA 3.1 7.2 + - - -
145B LYS* 3.3 13.2 + - - -
147B ILE* 1.3 81.0 - - - +
149B ALA* 1.3 61.5 + - - +
240B HIS* 4.3 7.8 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il